Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here we conduct a literature review examining temporal trends in code sharing in ecology and evolution publications since 2010, and test for an influence of code sharing on citation rate. We find that there is wide room for improvement in sharing code, as scientists are overwhelmingly (95%) failing to publish their code and that there has been no significant improvement over time. We also determined that there is a significant incentive to share, as we additionally find that code sharing can considerably improve citations, particularly when combined with open-access publication.

1. Prey metabarcoding has become a popular tool in molecular ecology for resolving trophic interactions at high resolution, from various sample types and animals. To date, most predator-prey studies of small-sized animals (<1 mm) have met the problem of overabundant predator DNA in dietary samples by adding blocking primers/peptide nucleic acids. These primers aim to limit the PCR amplification and detection of the predator DNA but may introduce bias to the prey composition identified by interacting with sequences that are similar to those of the predator. 2. Here we demonstrate the use of an alternative method to explore the prey of small marine copepods using whole-body DNA extracts and deep, brute force metabarcoding of an 18S rDNA fragment. 3. After processing and curating raw data from two sequencing runs of varying depth (0.4 and 5.4 billion raw reads), we isolated 1.3 and 52.2 million prey reads, with average depths of ~15 900 and ~120 000 prey reads per copepod individual, respectively. While data from both sequencing runs were sufficient to distinguish dietary compositions from disparate seasons, locations and copepod species, greater sequencing depth led to better separation of clusters. 4. As computation and sequencing are becoming ever more powerful and affordable, we expect the brute force approach to become a general standard for prey metabarcoding, as it offers a simple and affordable solution to consumers that are impractical to dissect or unknown to science.

Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub-patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analysed the largest collection of P. vivax genomes to date, including 1474 high-quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided in sub-populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility -- crucial for the parasite's survival in diverse environments. Understanding these population-level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.

1. Secondary metabolites produced by primary producers have a wide range of functions as well as indirect effects outside the scope of their direct target. Research suggests that protease inhibitors produced by cyanobacteria influence grazing by herbivores and may also protect against parasites of cyanobacteria. In this study we asked whether those same protease inhibitors produced by cyanobacteria also can influence interactions of herbivores with their parasites. 2. We used the Daphnia-Metschnikowia zooplankton host-fungal parasite system to address this question because it is well documented that cyanobacteria protease inhibitors suppress trypsin and chymotrypsin in the gut of Daphnia, and because it is known that Metschnikowia infects via the gut. We tested the hypothesis that Daphnia gut proteases are necessary for Metschnikowia spores to be released from their asci. We then also tested whether diets that decrease trypsin and chymotrypsin activity in the guts of Daphnia lead to lower levels of infection. 3. Our results show that chymotrypsin promotes release of the fungal spores from their asci. Moreover, a diet that strongly inhibited chymotrypsin activity in Daphnia decreased infection levels, particularly in the most susceptible Daphnia clones. 4. Our results support the growing literature that cyanobacterial diets can be beneficial to zooplankton hosts when challenged by parasites and uncover a mechanism that contributes to the protective effect of cyanobacterial diets. Specifically, we demonstrate that host chymotrypsin enzymes promote dehiscence of Metschnikowia spores; when cyanobacteria inhibit activity of chymotrypsin in hosts, this most likely traps the spore inside the ascus, preventing the parasite from puncturing the gut and beginning the infection process. 5. This study illustrates how secondary metabolites of phytoplankton can protect herbivores against their own enemies.

Parentage analyses via molecular markers have revealed multiple paternity within the broods of polytocous species, reshaping our understanding of animal behavior, ecology, and evolution. In a meta-analysis of multiple paternity in bird and mammal species, we conducted a literature search and found 138 bird and 64 mammal populations with microsatellite DNA paternity results. Bird populations averaged 19.5% multiple paternity and mammals more than twice that level (46.1%). We used a Bayesian approach to construct a null model for how multiple paternity should behave at random among species, under the assumption that all mated males have equal likelihood of siring success, given mean brood size and mean number of sires. We compared the differences between the null model and actual probabilities of multiple paternity. While a few bird populations fell close to the null model, most did not, averaging 34.0-percentage points below null model predictions; mammals had an average probability of multiple paternity 13.6-percentage points below the null model. Differences between bird and mammal species were also subjected to comparative phylogenetic analyses that generally confirmed our analyses that did not adjust for estimated historical relationships. Birds exhibited extremely low probabilities of multiple paternity, not only compared to mammals, but relative to other major animal taxa. The generally low probability of multiple paternity in birds might be produced by a variety of factors, including behaviors that reflect sexual selection (extreme mate guarding or unifocal female choice) and sperm competition (e.g., precedence effects favoring fertilization by early or late matings).

Herbarium specimens are increasingly being used as sources of information to understand the ecology and evolution of plants and their associated microbes. Most studies have used specimens as a source of genetic material using culture independent approaches. We demonstrate that herbarium specimens can also be used to culture nodule-associated bacteria, opening the possibility of using specimens to understand plant-microbe interactions at new spatiotemporal scales. We used historic and contemporary nodules of a common legume, Medicago lupulina, to create a culture collection. We were able to recover historic bacteria in 15 genera from three specimens (collected in 1950, 2004, and 2015). This work is the first of its kind to isolate historic bacteria from herbarium specimens. Future work should include inoculating plants with historic strains to see if they produce nodules and if they affect plant phenotype and fitness. Although we were unable to recover any Ensifer, the main symbiont of Medicago lupulina, we recovered some other potential nodulating species, as well as many putative growth-promoting bacteria.

Anthropogenic pressures on nature have been causing population declines for centuries. Intensified persecution of apex predators, like the golden eagle, resulted in population bottlenecks during the 19th-20th centuries. To study population genetics and demographic history of the golden eagle throughout its distribution, we collected museum samples from previously underrepresented regions, such as Russia and Central Asia. We used 12 microsatellite loci and a fragment of the mitochondrial DNA control region to re-evaluate phylogeography of Eurasian golden eagles and study the impacts of the population bottleneck. Our results revealed a north-south genetic gradient, expressed by the difference of Mediterranean and Holarctic lineages, as well as genetically distinct Northern Europe and Central Asia and Caucasus regions. Furthermore, Northern Europe exhibited the lowest, whereas Central Asia and Caucasus had the highest genetic diversity. Although golden eagles maintained relatively high genetic diversity, we detected genetic signatures of the recent bottleneck, including reduced genetic diversity and a decline in the effective female population size around the year 1975. Our study improves the knowledge of the genetic composition of Eurasian golden eagles and highlights the importance of understanding their historical population dynamics in the face of ongoing and future conservation efforts.

Gamete traits can vary widely among species, populations and individuals, influencing fertilisation dynamics and overall reproductive fitness. Sexual selection can play an important role in determining the evolution of gamete traits with local environmental conditions determining the strength and direction of sexual selection. Here we test for signatures of post-mating selection on gamete traits in relation to population density, and possible interactive effects of population density and sperm concentration on sperm motility and fertilisation rates among natural populations of mussels. Our study shows that males from high density populations produce smaller sperm compared with males from low density populations, but we detected no effect of population origin on egg size. Our results also reveal that females from low density populations tended to exhibit lower fertilisation rates across a range of sperm concentrations, although this became less important as sperm concentration increased. Variances in fertilisation success were higher for females than males and the effect of gamete compatibility between males and females increases as sperm concentrations increase. These results suggest that local population density can influence gamete traits and fertilisation dynamics but also highlight the importance of phenotypic plasticity in governing sperm-egg interactions in a highly dynamic selective environment.

Quantitative evidence on tree space segregation among avian assemblages in temperate primeval forests is currently lacking. Therefore, our study aimed to determine the species composition of birds across different parts of trees. We investigated whether species richness differs between positions on a tree and how these positions influence the probability of occurrence of specific bird species. To achieve this, we observed birds within permanent plots in Białowieża National Park (BNP) and analyzed the distribution patterns of birds within six vertical and three horizontal sectors of trees. The compositional dissimilarity between tree sectors was assessed using detrended correspondence analysis. We employed generalized linear mixed-effects models to examine differences in species richness and the probability of occurrence for ten of the most frequently observed species across tree sectors. The majority of the BNP bird community was associated with the branches, while other birds occupied the tree crown trunks and the understory trunks. Species richness was the highest on branches in the crown part of trees, followed by lower species richness on trunks associated with crowns, and the lowest richness was observed on branches and trunks in the understory. These results indicate that branches in the middle and lower parts of the crown serve as avian diversity hotspots on trees, likely due to the abundance of various food sources. The differing patterns of tree usage by specific bird species may suggest the avoidance of interspecific competition for resources. Importantly, our study provides a pristine state for future investigations.

Fish communities of streams and rivers might substantially be subsidized by terrestrial insects that fall into the water. Although such animal-mediated fluxes are increasingly recognized, little is known on how anthropogenic perturbations may influence the strength of such exchanges. Intense land-use, such as lignite mining may impact a river ecosystem due to the flocculation of iron (III) oxides, and thus altering food web dynamics. We compared sections of the Spree River in North-East Germany that were greatly influenced by iron oxides with sections located downstream of a dam where passive remediation technologies are applied. Compared to locations downstream of the dam, the abundance of benthic macroinvertebrates at locations of high iron concentrations upstream of the dam was significantly reduced. Similarly, catch per unit effort of all fishes was significantly higher in locations downstream of the dam compared to locations upstream of the dam and condition of juvenile and adult piscivorous pike Esox lucius were significantly lower in size in sections of high iron concentrations. Using an estimate of short-term (i.e., metabarcoding of the gut content) as well as longer-term (i.e., hydrogen stable isotopes) resource use, we could demonstrate that two of the three most abundant fish species, perch Perca fluviatilis, and bleak Alburnus alburnus, received higher contributions of terrestrial insects to their diet at locations of high iron concentration. In summary, lotic food webs upstream and downstream of the dam greatly differed in the overall structure with respect to the energy available for the highest tropic levels and the contribution of terrestrial insects to the diet of omnivorous fish. Therefore, human-induced environmental perturbation such as river damming and mining activities represent strong pressures that can alter the flow of energy between aquatic and terrestrial systems, indicating a broad impact on the landscape level.

A document by Giovanna Bonadonna. Click on the document to view its contents.

Personality variation, defined as among-individual differences in behaviour that are repeatable across time and context, is widely reported across animal taxa. From an evolutionary perspective, characterising the amount and structure of this variation is useful since differences among individuals are the raw material for adaptive behavioural evolution. However, behavioural variation among-individuals also has implications for more applied areas of evolution and ecology – from invasion biology, to ecotoxicology, and selective breeding in captive systems. Here, we investigate the structure of personality variation in the red cherry shrimp, Neocaridina heteropoda, a popular ornamental species that is readily kept and bred under lab conditions and is emerging as a decapod crustacean model across these fields, but for which basic biological, ecological, and behavioural data is limited. Using two assays and a repeated measures approach, we quantify behaviours putatively indicative of shy-bold variation and test for sexual dimorphism and/or size-dependent behaviours (as predicted by some state-dependent models of personality). We find moderate to high behavioural repeatabilities across traits. Although strong individual-level correlations across behaviours are consistent with a major personality axis underlying these observed traits, the multivariate structure of personality variation does not fully match a priori expectations of a shy-bold axis. This may reflect our ecological naivety with respect to what really constitutes bolder, more risk prone, behaviour in this species. We find no evidence for sexual dimorphism and only weak support size-dependent behaviour. Our study contributes to the growing literature describing behavioural variation in aquatic invertebrates. Furthermore, it lays a foundation for further studies harnessing the potential of this emerging model system. In particular, this existing behavioural variation could be functionally linked to life-history traits, invasive success, and serve as target of artificial selection or bioassays. It thus holds significant promise in applied research across ecotoxicology, aquaculture, and invasion biology.

“Coexistence frontiers”, or regions where human infrastructure and activity are increasing rapidly or newly appearing, constitute novel environments where wildlife must learn to navigate and coexist with people. It is widely recognized that behaviorally flexible species are more likely to persist in these human-dominated landscapes. Nevertheless, we do not fully understand how these animals navigate landscapes shaped by infrastructure, human activity, and human tolerance. As a widely reviled and behaviorally plastic apex predator, the spotted hyena (Crocuta crocuta) is a model species for understanding how wide-ranging large carnivores navigate social-ecological landscapes in an urbanizing world. Using high-resolution (minimum 5-min fix rates) GPS collar data and supplemental camera trap imagery, we applied resource selection and step selection functions to assess spotted hyena landscape navigation and fine-scale movement decisions in relation to social-ecological features in Lake Nakuru National Park and Soysambu Conservancy, Kenya. Second, we used camera traps and barrier behavior analysis (BaBA) to further examine hyena interactions with barriers. Our results show that environmental covariates—including NDVI, terrain, and proximity to water—were the best predictors of landscape-scale resource selection by hyenas, while human infrastructure and the likelihood of conflict with humans or livestock predicted fine-scale hyena movement decisions. We also found that hyena selection for these characteristics changed seasonally and across land management types. Camera traps documented an exceptionally high number of individual spotted hyenas (234) approaching the national park fence at 16 sites during the study period, and BaBA results suggested that hyenas perceive protected area boundaries’ electric fences as risky but may cross them out of necessity. Our results highlight that wildlife adaptability in coexistence frontiers may be expressed differently depending on context and scale. These results also point to the need to incorporate societal factors into multiscale analyses of carnivore movement to effectively plan for human-carnivore coexistence.

Intraspecific variation in plants is expected to have profound impacts on the arthropod communities associated with them. Because sexual dimorphism in plants is expected to provide consistent variation among individuals of the same species, researchers have often studied the effect it has on associated arthropods. Nevertheless, most studies have focused on the effect of sexual dimorphism in a single or a few herbivores, thus overlooking the potential effects on the whole arthropod community. Our main objective was to evaluate effects of Buddleja cordata’s plant-sex on its associated arthropod community. We surveyed 13 pairs of male and female plants every two months during a year (June 2010-April 2011). Every sampling date, we measured plant traits (water content and leaf thickness), herbivory, and the arthropod community. We did not find differences in herbivory between plant sex or through time. However, we found differences in water content through time, with leaf water-content matching the environmental seasonality. For arthropod richness, we found 68 morphospecies associated with female and 72 with male plants, from which 53 were shared by both sexes. We did not observe differences in morphospecies richness; however, we found sex-associated differences in the diversity of all species and differences on the diversity of the most abundant species with an interesting temporal component. During peak flowering season male plants showed higher values on both parameters, but during the peak fructification season female plants showed the higher values on both diversity parameters. Our research exemplifies the interaction between plant-phenology and plant-sex as drivers of arthropod communities’ diversity, even when plant sexual-dimorphism is inconspicuous, and highlighting the importance of accounting for seasonal variation. We stress the need of conducting more studies that test this time-dependent framework in other dioecious systems, as it has the potential to reconcile previous contrasting observations reported in the literature.

PREMISE OF THE STUDY Plant reproductive failure is a critical concern for conserving rare and endangered species that typically have low-density and sparse populations. One important factor contributing to reproductive failure is the spatial arrangement of plants within a population, which can lead to isolation and negatively affect seed output, particularly in obligate outcrossers. Additionally, this effect can be compounded by plant size. Here, we investigate how plants’ spatial distribution and size influence the reproductive success of Carica chilensis, a threatened papaya species. METHODS Using flower exclusion, we first examined whether C. chilensis can produce seeds via apomixis. We then used Spatial Point Pattern Analysis (SPPA) in three populations to examine the spatial arrangement of plants and, finally, we assess whether plant size and mate distance influence the reproductive success of this plant species. KEY RESULTS C. chilensis is a dioecious shrub unable to produce fruits through apomixis. The SPPA revealed significant clustering of female and male plants at different spatial scales, indicating a non-random distribution. Moreover, a significant attraction between the sexes suggested a preference for proximity. In two populations, closer proximity to male plants was linked to higher seed production. CONCLUSIONS Our study revealed that the absence of apomixis in C. chilensis makes it prone to experiencing distance-dependent reproductive failure. In particular, the seed set was compromised in female plants isolated from male neighbors. This link between isolation and seed production was especially significant in the driest site, and we discuss how environmental factors can exacerbate this effect.

1. Graphs in research articles can increase the comprehension of statistical data but may mislead readers if poorly designed. Previous literature has found that the two most frequently used plot types - bar charts and dot and whisker plots - are a poor way to represent data because they only show the summary statistics of data, not their distribution, potentially hiding important information. 2. Calls have been made encouraging abandonment of bar charts and the use of more informative plot types, such as boxplots, violin plots, univariate scatter plots, and dot plots. We compare these plot types to assess their relative strengths and weaknesses to represent four different distributions of the data commonly observed in biological studies, finding that all the assessed plot types are either difficult to read at large sample sizes or misrepresent certain distributions of data. 3. We present an analysis of the plot types used in four ecology and conservation journals covering multiple areas of these research fields, finding widespread use of uninformative bar charts and dot and whisker plots (60 % of all plots showing one-dimensional data from multiple groups for the purpose of comparison). Some articles presented more informative figures by combining plot types, generally boxplots and a second layer such as a flat violin plot, to better display the data. This shows an appetite for more effective plot types within conservation and ecology, which may further increase if an accurate and user-friendly plot types were made available. 4. In response to this, we propose sea stack plots, which combine vertical histograms and summary statistics, and allow for an accurate representation of different data distributions, thereby largely overcoming the weaknesses associated with other alternatives to uninformative plots. We provide a tool to create sea stack plots with our R package ‘seastackplot’, available through GitHub.

Interactions among coexisting mesocarnivores can be influenced by different factors such as the presence of large carnivores, land-use, environmental productivity, or human disturbance. Disentangling the relative importance of bottom-up and top-down processes can be challenging, but it is important for biodiversity conservation and wildlife management. The aim of this study was to assess how the interactions among mesocarnivores (red fox Vulpes vulpes, badger Meles meles, and pine marten Martes martes) are affected by large carnivores (Eurasian lynx Lynx lynx and wolf Canis lupus), land cover variables (proportion of agricultural land and primary productivity), and human disturbance, as well as how these top-down and bottom-up mechanisms are influenced by season. We analyzed three years (2018-2020) of camera trapping data from Norway and used structural equation models to assess hypothesized networks of causal relationships. Our results show that land cover variables are stronger predictors of mesocarnivore activity than large carnivores in Norway. This might be caused by a combination of low density of large carnivores in an unproductive ecosystem with strong seasonality. Additionally, all mesocarnivores showed positive interactions among each other, which were stronger in winter. The prevalence of positive interactions among predators might indicate a tendency to use the same areas and resources combined with weak interference competition. Alternatively, it might indicate some kind of facilitative relationship among species. Human disturbance had contrasting effects for different species, benefiting the larger mesocarnivores (red fox and badger) probably through food subsidization, but negatively affecting apex predators (wolf and lynx) and smaller mesocarnivores (pine marten). In a human-dominated world, this highlights the importance of including anthropogenic influences in the study of species interactions.

Cymbaria L. is a small genus nearly endemic to the Mongolian Plateau with only two hemiparasitic species. Cymbaria daurica L. is an important herb “Xinba” in traditional Mongolian medicine. However, C. daurica is often confused with its sister species Cymbaria mongolica Maxim. because they only differ in anther morphology. In addition, phylogenetic placement and reductive evolution of this genus within the Orobanchaceae remain poorly resolved. Here, we firstly sequenced two Cymbaria chloroplast genomes and then conducted a comparative analysis among those of 54 Orobanchaceae species. We found that the chloroplast genomes of Cymbaria species were characterized by pseudogenization/loss events of eight ndh genes and a unique rbcL-matK inversion. Unlike the high-variability observed in holoparasites, Cymbaria and other hemiparasites exhibited high similarity to autotrophs in genome size, GC content, and intact genes. Notely, four pairs of specific DNA barcodes (CymN1, CymN2, CymY, and CymR) were developed to distinguish the herb C. daurica from its adulterant C. mongolica. Phylogenetic analyses revealed that genus Cymbaria and the Schwalbea-Siphonostegia clade were grouped into the tribe Cymbarieae. This tribe formed an independent sister clade to the remaining parasitic lineages. Furthermore, the diversification of monophyletic Cymbaria occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. These findings provide valuable information for regarding taxonomy, phylogeny and evolution of Cymbaria and can be used to validate the authenticity of the herb “Xinba”.